[BioC] Long Time Series analysis
mjonczyk at biol.uw.edu.pl
Wed Aug 18 10:38:51 CEST 2010
> Date: Wed, 11 Aug 2010 21:12:04 -0700 (PDT)
> From: Xiaokuan Wei <weixiaokuan at yahoo.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Long Time Series analysis
> Dear List,
> I?was using?maSigPro for time series analysis of microarray.?I
> have about 12
> time points for a yeast data, and each time point only has two
> replicates. I am
> wondering if I can use quadratic model?to perform the analysis. If I
> used higher
> order model, will overfitting become a problem?
I've done analysis of time-course experiment with seven points, I
considered to use 3rd or 4th order polynomial. Eventually it turned out
that 3rd order is enought, 4th order gives nothing new.
I advise you to try with quadratic model, 3rd, 4th and maybe higer order
polynomial too and to look if it gives different results, if not lower
level polynomial is enought.
> I noticed that in?maSigPro tutorial, 4.4 mentioned "Long Time
> Series". But it
> has no detailed explaination. Does Ana or someone can share?some
> examples I can
> follow for such analysis?
I've asked for longer than mentioned 5 time points series and I've been
informed that in case of 7 time points I can use normal workflow.
> Any other packages I can use for a long time series analysis?
You can look in "packages" section at the Bioconductor website.
Hope it helps somehow.
> Your help will be greatly appreciated.
> Thanks again.
Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1
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